text: from bayes_implicit_solvent.solvation_free_energy import beta, construct_gbsa_force, get_vacuum_samples, create_implicit_sim, get_implicit_u_diffs, predict_solvation_free_energy
  
  import numpy as np
  
  import pytest
  
  from openmmtools.testsystems import AlanineDipeptideVacuum
  
  @pytest.fixture
  def alaninedipeptide_testsystem():
      testsystem = AlanineDipeptideVacuum()
      return testsystem
  
  def test_construct_gbsa_force(alaninedipeptide_testsystem):
      """Assert that constructing"""
      system = alaninedipeptide_testsystem.system
      gbsa_force = construct_gbsa_force(system)
      assert("GBSA" in gbsa_force.__class__.__name__)
  
  # TODO: Also test what happens if there already is a GBSA force in system...
  
  def test_get_vacuum_samples(alaninedipeptide_testsystem):
      a = alaninedipeptide_testsystem
      n_samples = 10
      vacuum_sim, vacuum_traj = get_vacuum_samples(a.topology, a.system, a.positions, n_samples=n_samples, thinning=10)
      vacuum_sim.step(1) # check that vacuum_sim has a step method and doesn't crash
      assert (len(vacuum_traj) == n_samples) # check we have the right number of samples
      assert ( len(vacuum_traj[0]) == len(a.positions)) # check the samples have the right shape
  
  from bayes_implicit_solvent.utils import get_gbsa_force
  def test_create_implicit_sim(alaninedipeptide_testsystem):
      """Check that we can create a simulation object with a GBSA force in force group 0,
      all other forces in group 1."""
      topology, system = alaninedipeptide_testsystem.topology, alaninedipeptide_testsystem.system
      implicit_sim = create_implicit_sim(topology, system)
  
      # check that implicit sim contains a GBSA force
      gbsa_force = get_gbsa_force(implicit_sim.system)
      assert ("GBSA" in gbsa_force.__class__.__name__)
  
      # check that the GBSA force is in group 0
      assert ( gbsa_force.getForceGroup() == 0 )
  
      # check that all other forces are in group 1
      for force in implicit_sim.system.getForces():
          if 'GBSA' not in force.__class__.__name__:
              assert ( force.getForceGroup() == 1)
  
  
  def test_get_implicit_u_diffs():
      """check that the function based on force groups computes the same reduced potential energy differences
      as directly computing beta * (U_implicit - U_vacuum)"""
  
      # TODO: Finish writing this test
      raise (NotImplementedError('must initialize vacuum_sim, implicit_sim, x'))
      vacuum_sim, implicit_sim, x = None, None, None
  
      u_diff = get_implicit_u_diffs(implicit_sim, x)
  
      u_diff_ref = np.zeros(len(x))
  
      for i in range(len(x)):
          vacuum_sim.context.setPositions(x[i])
          implicit_sim.context.setPositions(x[i])
  
          U_implicit = implicit_sim.context.getState(getEnergy=True).getPotentialEnergy()
          U_vacuum = vacuum_sim.context.getState(getEnergy=True).getPotentialEnergy()
          u_diff_ref[i] = beta * (U_implicit - U_vacuum)
  
          u_diff_ref[i] = beta * implicit_sim.context.getState(getEnergy=True, groups={0}).getPotentialEnergy()
  
      np.testing.assert_allclose(u_diff, u_diff_ref)
  